Aligments for a candidate for pccB in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Aligments for a candidate for pccB in Marinobacter adhaerens HP15

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate GFF2594 HP15_2538 acetyl/propionyl-CoA carboxylase beta subunit

Query= metacyc::MONOMER-17283
         (535 letters)



>lcl|FitnessBrowser__Marino:GFF2594 HP15_2538 acetyl/propionyl-CoA
           carboxylase beta subunit
          Length = 538

 Score =  424 bits (1091), Expect = e-123
 Identities = 227/545 (41%), Positives = 326/545 (59%), Gaps = 17/545 (3%)

Query: 1   MSIIHSHIQPNSPDFQAN---FAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVR 57
           M ++ S +   S DF+ N      H +   D+ +++  + +      R +  +RGKL  R
Sbjct: 1   MQVLESTVSSTSEDFRTNAEAMDAHITTFRDVEQKVLDLAEAA----REKFTKRGKLLPR 56

Query: 58  DRIDTLIDPDSSFLEIGALAAYNVYDEE---VPAAGIVCGIGRVAGRPVMIIANDATVKG 114
           DRI+ L+D  + FLE+ +LA Y ++D++   +   GI+ GIG V+G   +++A+++ +KG
Sbjct: 57  DRINRLLDRGTPFLELCSLAGYKMHDDKDGSLAGGGIIAGIGYVSGIRCLVVASNSAIKG 116

Query: 115 GTYFPLTVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMS 174
           GT  P  + K LR Q+IA EN+LP + L +SGGA L   +++F       R F NQA+MS
Sbjct: 117 GTITPAGLDKTLRLQQIAMENKLPVVSLSESGGANLNYATDIFVLG---ARGFANQARMS 173

Query: 175 AEGIPQIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGG 234
           A GIPQ+  V G+ TAGGAY P +SD V++V+    +FL GPPL+KAATGE  T EELGG
Sbjct: 174 AAGIPQVTVVHGNATAGGAYQPGLSDYVIVVREQAKMFLAGPPLLKAATGEVATDEELGG 233

Query: 235 ADVHTRISGVADYFANDDREALAIVRDIVAHLGPRQRAN-WELRDPEPPRYDPREIYGIL 293
           A++H  ++G A+Y A DD + +   R+I+  L   ++   W     E P Y   E+ G++
Sbjct: 234 AEMHATVAGTAEYLAEDDADGIRQARNILEALPWNEQLQPWRELQWEEPLYPADELLGVI 293

Query: 294 PRDFRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESA 353
           P D ++ YDVRE++ARI DGS+  +FK  +    VCG   IEG  VGI+ NNG +    +
Sbjct: 294 PADSKKPYDVREILARIADGSKFMDFKNEFDDQTVCGTIRIEGHSVGIIGNNGPITPAGS 353

Query: 354 LKGAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVII 413
            K A FI+LC     PL+FL N TGFMVG   E  GI K G+K++ AV+   VPK  ++I
Sbjct: 354 AKAAQFIQLCDQAGTPLLFLHNTTGFMVGTHSEQNGIIKHGSKMIQAVANCRVPKVAIVI 413

Query: 414 GGSFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEE 473
           GGS+GAGNY MCGR   PR ++ WPN+R +VMG  QA  V+  +  D  R  G +  P+ 
Sbjct: 414 GGSYGAGNYAMCGRGLDPRFIFAWPNSRTAVMGPAQAGKVMRIVAEDKQRRGGMEPDPKT 473

Query: 474 QERFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEA---PVQPTRF 530
            +        K E+     + +ARLWDDG+IDP +TRRVLAL L    EA    ++P  F
Sbjct: 474 LDFLEQATAKKLEEGSTALFGTARLWDDGLIDPRDTRRVLALVLDVCREAEARQLRPNTF 533

Query: 531 GVFRM 535
           GV R+
Sbjct: 534 GVARL 538


Lambda     K      H
   0.322    0.139    0.423 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 768
Number of extensions: 43
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 535
Length of database: 538
Length adjustment: 35
Effective length of query: 500
Effective length of database: 503
Effective search space:   251500
Effective search space used:   251500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources